Automated methods for quantitating plaque formation in experimental animals and its location along the arterial tree for statistical correlation with other quantitative factors such as breed, age, diet, etc. are required. Specimen preparation, image digitization, image transformation to a standard reference coordinate system and disease detection procedures are all fully operational. This method reduces processing time 300 fold over former manual methods and assures reproducibility. Resulting topographic maps describe disease in a concise and quantitative manner, providing a tool for correlation of disease patterns with local histologic, physical, and biochemical events.